Characterization of Multi-Charge Mass Spectra for Peptide Sequencing. - Ket Fah Chong; Kang Ning 001; Hon Wai Leong; Pavel A. Pevzner (APBC, 2006)

Finding Patterns in Biological Sequences by Longest Common Subsequencesand Shortest Common Supersequences. - Kang Ning 001; Hoong Kee Ng; Hon Wai Leong (BIBE, 2006)

Towards a Better Solution to the Shortest Common Supersequence Problem: A Post. - Kang Ning 001; Hon Wai Leong (IMSCCS (1), 2006)

Automated Identification of Protein Classification and Detection of Annotation Errors in Protein Databases Using Statistical Approaches. - Kang Ning 001; Hon Nian Chua (KDLL, 2006)

A Database Search Algorithm for Identification of Peptides with Multiple Charges Using Tandem Mass Spectrometry. - Kang Ning 001; Ket Fah Chong; Hon Wai Leong (BioDM, 2006)

Towards a better solution to the shortest common supersequence problem: the deposition and reduction algorithm. - Kang Ning 001; Hon Wai Leong (BMC Bioinform., 2006)

Modeling and Characterization of Multi-charge Mass Spectra for Peptide Sequencing. - Ket Fah Chong; Kang Ning 001; Hon Wai Leong; Pavel A. Pevzner (J. Bioinform. Comput. Biol., 2006)

De Novo Peptide Sequencing for Mass Spectra Based on Multi-Charge Strong Tags. - Kang Ning 001; Ket Fah Chong; Hon Wai Leong (APBC, 2007)

A New Approach for Similarity Queries of Biological Sequences in Databases. - Hoong Kee Ng; Kang Ning 001; Hon Wai Leong (PAKDD, 2007)

Detecting hubs and quasi cliques in scale-free networks. - Sriganesh Srihari; Hoong Kee Ng; Kang Ning 001; Hon Wai Leong (ICPR, 2008)

Using Indirect protein-protein Interactions for protein Complex Prediction. - Hon Nian Chua; Kang Ning 001; Wing-Kin Sung; Hon Wai Leong; Limsoon Wong (J. Bioinform. Comput. Biol., 2008)

On Preprocessing and Antisymmetry in de novo peptide Sequencing: Improving Efficiency and Accuracy. - Kang Ning 001; Nan Ye; Hon Wai Leong (J. Bioinform. Comput. Biol., 2008)

A Deposition and Post Processing Approach for the Longest Common Subsequence Problem - Kang Ning 001 (CoRR, 2009)

A Pseudo DNA Cryptography Method - Kang Ning 001 (CoRR, 2009)

The Distribution and Deposition Algorithm for Multiple Sequences Sets - Kang Ning 001; Hon Wai Leong (CoRR, 2009)

The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment. - Kang Ning 001; Alexey I. Nesvizhskii (BMC Bioinform., 2010)

Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. - Kang Ning 001; Hoong Kee Ng; Sriganesh Srihari; Hon Wai Leong; Alexey I. Nesvizhskii (BMC Bioinform., 2010)

MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure. - Sriganesh Srihari; Kang Ning 001; Hon Wai Leong (BMC Bioinform., 2010)

Deposition and extension approach to find longest common subsequence for thousands of long sequences. - Kang Ning 001 (Comput. Biol. Chem., 2010)

Multiple oligo nucleotide arrays: Methods to reduce manufacture time and cost. - Kang Ning 001 (CoRR, 2010)

An Open-source Collaboration Environment for Metagenomics Research. - Xiaoquan Su; Yongzheng Ma; Hongwei Yang; Xingzhi Chang; Kai Nan; Jian Xu 020; Kang Ning 001 (eScience, 2011)

Analysis of the relationships among Longest Common Subsequences, Shortest Common Supersequences and patterns and its application on pattern discovery in biological sequences. - Kang Ning 001; Hoong Kee Ng; Hon Wai Leong (Int. J. Data Min. Bioinform., 2011)

The multiple sequence sets: problem and heuristic algorithms. - Kang Ning 001; Hon Wai Leong (J. Comb. Optim., 2011)

A machine learning framework of functional biomarker discovery for different microbial communities based on metagenomic data. - Wei Fang; Xingzhi Chang; Xiaoquan Su; Jian Xu 020; Deli Zhang; Kang Ning 001 (ISB, 2012)

Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data. - Xiaoquan Su; Jian Xu 020; Kang Ning 001 (Bioinform., 2012)

SNP calling using genotype model selection on high-throughput sequencing data. - Na You; Gabriel H. Murillo; Xiaoquan Su; Xiaowei Zeng; Jian Xu 020; Kang Ning 001; Shoudong Zhang; Jiankang Zhu; Xinping Cui (Bioinform., 2012)

Parallel-META: efficient metagenomic data analysis based on high-performance computation. - Xiaoquan Su; Jian Xu 020; Kang Ning 001 (BMC Syst. Biol., 2012)

Systematic assessment of the expected length, variance and distribution of Longest Common Subsequences. - Kang Ning 001; Kwok Pui Choi (CoRR, 2013)

GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU. - Xiaoquan Su; Xuetao Wang; Gongchao Jing; Kang Ning 001 (Bioinform., 2014)

Microbial community pattern detection in human body habitats via ensemble clustering framework. - Peng Yang; Xiaoquan Su; Le Ou-Yang; Hon Nian Chua; Xiaoli Li 001; Kang Ning 001 (BMC Syst. Biol., 2014)

DNA Extraction Protocol for Biological Ingredient Analysis of Liuwei Dihuang Wan. - Xinwei Cheng; Xiaohua Chen; Xiaoquan Su; Huanxin Zhao; Maozhen Han; Cunpei Bo; Jian Xu 020; Hong Bai; Kang Ning 001 (Genom. Proteom. Bioinform., 2014)

Meta-QC-Chain: Comprehensive and Fast Quality Control Method for Metagenomic Data. - Qian Zhou; Xiaoquan Su; Gongchao Jing; Kang Ning 001 (Genom. Proteom. Bioinform., 2014)

The Tara Oceans Project: New Opportunities and Greater Challenges Ahead. - Houjin Zhang; Kang Ning 001 (Genom. Proteom. Bioinform., 2015)

Application of Meta-Mesh on the analysis of microbial communities from human associated-habitats. - Xiaoquan Su; Xiaojun Wang; Gongchao Jing; Shi Huang; Jian Xu 020; Kang Ning 001 (Quant. Biol., 2015)

Condensing Raman spectrum for single-cell phenotype analysis. - Shiwei Sun; Xuetao Wang; Xin Gao 001; Lihui Ren; Xiaoquan Su; Dongbo Bu; Kang Ning 001 (BMC Bioinform., 2015)

MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data. - Gabriel H. Murillo; Na You; Xiaoquan Su; Wei Cui; Muredach P. Reilly; Mingyao Li; Kang Ning 001; Xinping Cui (Bioinform., 2016)

FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. - Chao Wang; Haicang Zhang; Wei-Mou Zheng; Dong Xu 002; Jianwei Zhu; Bing Wang; Kang Ning 001; Shiwei Sun; Shuai Cheng Li 001; Dongbo Bu (Bioinform., 2016)

Strain-GeMS: optimized subspecies identification from microbiome data based on accurate variant modeling. - Chongyang Tan; Wei Cui; Xinping Cui; Kang Ning 001 (Bioinform., 2019)

Meta-network: optimized species-species network analysis for microbial communities. - Pengshuo Yang; Shaojun Yu; Lin Cheng; Kang Ning 001 (BMC Genom., 2019)

Stereotypes About Enterotype: the Old and New Ideas. - Mingyue Cheng; Kang Ning 001 (Genom. Proteom. Bioinform., 2019)

Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake. - Maozhen Han; Melissa Dsouza; Chunyu Zhou; Hongjun Li; Junqian Zhang; Chaoyun Chen; Qi Yao; Chaofang Zhong; Hao Zhou; Jack A. Gilbert; Zhi Wang; Kang Ning 001 (Genom. Proteom. Bioinform., 2019)

The Fast Track for Microbiome Research. - Kang Ning 001; Yigang Tong (Genom. Proteom. Bioinform., 2019)

Classification of the Gut Microbiota of Patients in Intensive Care Units During Development of Sepsis and Septic Shock. - Wang-Lin Liu; Mingyue Cheng; Jinman Li; Peng Zhang; Hang Fan; Qinghe Hu; Maozhen Han; Longxiang Su; Huaiwu He; Yigang Tong; Kang Ning 001; Yun Long (Genom. Proteom. Bioinform., 2020)

Hydrogen bonds meet self-attention: all you need for protein structure embedding. - Cheng Chen; Yuguo Zha; Daming Zhu; Kang Ning 001; Xuefeng Cui (BIBM, 2021)

Meta-Prism: Ultra-fast and highly accurate microbial community structure search utilizing dual indexing and parallel computation. - Mo Zhu; Kai Kang; Kang Ning 001 (Briefings Bioinform., 2021)

Reliable and Interpretable Mortality Prediction With Strong Foresight in COVID-19 Patients: An International Study From China and Germany. - Tao Bai; Xue Zhu; Xiang Zhou; Denise Grathwohl; Pengshuo Yang; Yuguo Zha; Yu Jin; Hui Chong; Qingyang Yu; Nora Isberner; Dongke Wang; Lei Zhang; et al. (Frontiers Artif. Intell., 2021)

EXPERT: transfer learning-enabled context-aware microbial community classification. - Hui Chong; Yuguo Zha; Qingyang Yu; Mingyue Cheng; Guangzhou Xiong; Nan Wang; Xinhe Huang; Shijuan Huang; Chuqing Sun; Sicheng Wu; Wei-Hua Chen; Luís Pedro Coelho; et al. (Briefings Bioinform., 2022)

Ontology-aware neural network: a general framework for pattern mining from microbiome data. - Yuguo Zha; Kang Ning 001 (Briefings Bioinform., 2022)

Microbial Dark Matter: from Discovery to Applications. - Yuguo Zha; Hui Chong; Pengshuo Yang; Kang Ning 001 (Genom. Proteom. Bioinform., 2022)

ContactLib-ATT: A Structure-Based Search Engine for Homologous Proteins. - Cheng Chen; Yuguo Zha; Daming Zhu; Kang Ning 001; Xuefeng Cui (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Tracing human life trajectory using gut microbial communities by context-aware deep learning. - Haohong Zhang; Hui Chong; Qingyang Yu; Yuguo Zha; Mingyue Cheng; Kang Ning 001 (Briefings Bioinform., 2023)

Artificial intelligence-enabled microbiome-based diagnosis models for a broad spectrum of cancer types. - Wei Xu; Teng Wang; Nan Wang; Haohong Zhang; Yuguo Zha; Lei Ji 006; Yuwen Chu; Kang Ning 001 (Briefings Bioinform., 2023)

Techniques for learning and transferring knowledge for microbiome-based classification and prediction: review and assessment. - Jin Han; Haohong Zhang; Kang Ning 001 (Briefings Bioinform., 2024)

Hidden Links Between Skin Microbiome and Skin Imaging Phenome. - Mingyue Cheng; Hong Zhou; Haobo Zhang; Xinchao Zhang; Shuting Zhang; Hong Bai; Yugo Zha; Dan Luo; Dan Chen; Siyuan Chen; Kang Ning 001; Wei Liu (Genom. Proteom. Bioinform., 2024)

PREDAC-FluB: predicting antigenic clusters of seasonal influenza B viruses with protein language model embedding based convolutional neural network. - Wenping Xie; Jingze Liu; Chuan Wang; Jiangyuan Wang; Wenjie Han; Yousong Peng; Xiangjun Du; Jing Meng; Kang Ning 001; Taijiao Jiang (Briefings Bioinform., 2025)